Merge branch 'master' of https://github.com/dmattek/shiny-timecourse-selector

README.md

+# Time-course analysis web-app
+
+#### Running the app from the server
+The app can be accessed here:
+http://pertzlab.unibe.ch:3838/shiny-timecourse-selector/
+
+#### Running the app locally
+Alternatively, after downloading the code, the app can be run within RStudio. Open `server.R` or `ui.R` file, then click "Run App" button with green triangle in the upper right corner of the window with code open.
+
+Following packages need to be installed in order to run the app locally:
+
+* shiny
+* shinyjs
+* data.table
+* ggplot2
+* gplots
+* plotly
+* d3heatmap
+* dendextend
+* RColorBrewer
+* sparcl
+* scales
+
+Install packages using `install.packages('name_of_the_package_from_the_list_above')` command in RStudio command line.
+
+#### Input file
+The app recognizes CSV (comma-separated values) files: data columns separated by a comma, floating point numbers using a dot (full-stop).
+
+The data file has to be in a so called long format, where individual time-courses (tracks) are arranged one after another. Note a wide-format where individual tracks are arranged in neighbouring columns is NOT supported!
+
+Sample few lines of the input file:
+
+`"Metadata_Series", "TrackObjects_Label", "Intensity_MeanIntensity_Ratio", "RealTime", "Stim_All_Ch", "Stim_All_S"`
+
+`0, 2, 1149.00311105531, 0, "Ch01: FGF 250 ng/ml 60min pulse", "S00: FGF 250 ng/ml 60min pulse"`
+
+`0, 3, 1160.43905280656, 0, "Ch01: FGF 250 ng/ml 60min pulse", "S00: FGF 250 ng/ml 60min pulse"`
+
+`0, 4, 1303.06046656558, 0, "Ch01: FGF 250 ng/ml 60min pulse", "S00: FGF 250 ng/ml 60min pulse"`
+
+The first row should include column headers. Necessary columns include:
+
+* Unique number of the field of view (FOV), here "Metadata_Series"
+* Unique identifier of track ID within the FOV, here "TrackObjects_Label"
+* Time point, here "RealTime"
+* Measurement column (can be many columns), here "Intensity_MeanIntensity_Ratio"
+
+Additionally, columns with condition names can be included. In the example above, "Stim_All_S" identifies condition per FOV, and "Stim_All_Ch" relates to a condition name within the well. These two columns are useful to group and plot time-courses in separate facets per FOV or per well.